After you finish the task pointed with a marker on map, you can use this simple way to remove used markers, and then create new ones on a clear map. So the effect is when you starting the game there is no markers, and as you go through a mission you can create and delete markers as it suit your needs.
VIDEO EXAMPLE
This is the simple script that you place in ON ACT field: " deleteMarker "marker1" "
You can use trigger or waypoints to delete marker in arma 3. Just bear in mind to remember the names of markers that you are creating and want to delete.
...BEFORE - AFTER...